Why is the dealer the absolute last resource people turn to with these cars? I'm sure they can tell you whether there is a software issue, I know of no hardware incompatibility......
It's possible you might need the dealer to update the software depending on the year of the transmission you find. I think this is a good idea for a high mileage car actually, and the direction I'll go if I need to with mine.
A visit to your dealer might give you everything you need to know before you go hunting for the parts......
